The human immunodeficiency virus type 1 (HIV-1) protease (PR) is one of five viral targets of highly active anti-retroviral therapy (HAART) administered to the 34 million individuals living with HIV. The viral protease is a critical targetas it is responsible for virion maturation via processing of the Gag-Pol polypeptide. Patient adherence to HAART regimens is crucial, as non-adherence leads to continuous viral replication. Viral replication escape and subsequent rebound impedes HAART treatment by allowing for the growth of viral populations bearing various resistant mutations. The mutations within viral drug targets, including the viral protease, allow for inhibition evasion and continued biological function. Understanding the mechanisms underlying severe drug resistance is a major hindrance in inhibitor development. Increasing mutation number is not directly proportional to the severity of resistance, suggesting that resistance is not simply additive but that it is interdependent. I propose that the culmination of physical amino acid properties, locations, and combinations of resistant mutations underlie interdependent nature of multi-drug resistance. To probe potential patterns that underlie the interdependent mechanisms of resistance in the viral protease, I will use a panel of five multi-drug resistance (MDR) proteases derived from patients. The proteases in this panel bear between 19-26 mutations each and are resistant to even the most potent protease inhibitors (PIs). Using an array of biochemical and biophysical techniques, I will determine the in vitro inhibition and thermodynamic profiles for each of the proteases in th panel. I will use X-Ray crystallography and molecular dynamics simulations to structurally and dynamically characterize the physical aspects of interdependent resistance patterns. In addition to the protease variants, I have also obtained their cognate substrates from NC to p6 of Gag (residues 407-488). I will use the patient-derived proteases and their corresponding substrates to determine how substrate recognition and processing is allowed to continue in the presence of inhibitors using the techniques described above. Discerning and taking advantage of the mechanisms that underlie multi-drug resistance in viral targets could provide the tools necessary to proactively meliorate both current treatment and inhibitor design for HIV-1 targets.